On a sidenote: I think a trained archer is deadlier than a musketeer, since he ignores most armor and has a high rate of fire... pull of some of the tricks that are available to bows and it gets nasty like hell.
The numbers are a little uneven for highly trained PCs, it's true. Let's consider two level 5 PCs with 5 relevant feats each (doable for soldiers and scouts), dex 16 and full BAB:
EDIT: Cleaned up now that I've checked the text of some feats, added stances.
Bob blackpowder carries three pistols and a bandolier, all his weapons and ammo have the superior and AP upgrades, and he has the Two Weapon Fighting, Quick Draw, Firearms Master, and, oh, let's say Black Powder Basics/Mastery feats (too low level to really benefit from Bulls Eye without them, and even with them, Firearms Master is better). He can fire 3 shots a round in the first round at a total of +8 to hit on each (5+3+1-2+1), each doing 3d6+1d4+2 (average 15) damage w AP 4. Then in each round after he can fire one shot at first +11, then +12, etc. to hit (assuming one target, and using the stance/bonus from black powder basics and mastery), doing a further 3d6+1d4+2 damage w AP 4. Each shot also has a good chance of knocking over the opponent, but that's rather tricky to factor in.
Bill the Bow on the other hand carries a longbow and a ton of standard arrows, all with the superior and AP upgrade. He has Bow Basics/Mastery/Supremacy, plus Rapid Fire and Bow Master (too low level to be able to hit well with the Blackened Sky combo). He can fire 9 shots per round, doing 1d6+1d4+4, avg 10 damage, with 3 shots on a net of +9 to hit, 3 on +5, and 3 on -1.
Now, let's say they're firing at a single large target with a total defence of 15. Ignoring criticals for now (whole other headache) Bob will be doing 15*3*0.65 damage on his first round (29.25), and 15*0.8 (12) damage the next round, with a marginal improvement in damage (0.75) each round after. Bill, meanwhile, will be doing 8*3*0.7 + 8*3*0.5 + 8*3*0.2 (total of 33.6 damage) each round; slightly better on the first round, and significantly better after that, albeit at a greater cost in ammo. Adding in stances made a significant difference; weirdly, Bob Blackpowder might have been better off going with Bow Basics than Black Powder Basics/Mastery, since it grants a stance with significantly more general utility (Focused Aim being best for when you've a long time to watch your target before firing, which is generally unlikely, and only really works at all with the Mastery ability).
The general power balance which this illustrates is aimed at the 17th/18th centuries, when highly trained archers > highly trained musketeers, but musketeers required much less training to be effective. Which is not to say that you couldn't make a perfectly effective Musketeer or Dragoon Soldier 4/Deadeye who plinks 2 or 3 opponents in the first round and 1 in each round after, just that they would be less scary than an Archer Soldier 4/Deadeye. Whereas a group of 10 NPCs with black powder weapons is much more scary (if potentially lucrative) to your PCs than 10 NPCs with bows, and a black powder weapon of some description can offer a significant boost on top of a bow or crossbow in ranged combat to a PC who doesn't want to invest more than a proficiency or two and some spare cash in it.
On the whole, bringing in 19th century technology like multiple-chambered firearms raises a whole load of other questions. E.g., are there also steamships, trains, etc. (Are you ending up in the realms of steampunk, or at least the wild west, in short). They don't have to, if you don't want them to, but it's something to think about.